[gmx-users] Rotation Constraints - PMF - external potential

Carsten Kutzner ckutzne at gwdg.de
Fri Jul 26 12:03:49 CEST 2013 

Hi Anna,

On Jul 26, 2013, at 11:17 AM, battistia at libero.it wrote:

> Dear Carsten,
> 
> thank you very much for your support!
> 
> At the beginning I did not follow your indications correctly but now, using 
> the orientation restraints and the indication in the paper
I think you do not need orientation restraints at all, just enforced rotation.

> 
> Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic 
> Simulations with GROMACS
> Kutzner C, Czub J, and Grubmüller H
> J. Chem Theory and Comp. 7: 1381-1393 (2011)
> 
> I believe I made it.  
> 
> Just few questions to be sure, if I can:
> how the vector v ( namely the axis rotation defined in the paper) is defined?
> giving a (large) number of atoms as rotation group, I suppose that the vector 
> u identify the center of mass of the group, and in this point the v vector 
> defines the direction that one gives with the  rot_vec entry in mdp file. Is it 
> correct?
Yes, the rotation vector v you provide in the mdp file as rot_vec0, and u
as rot_pivot0. It depends a bit on the rotation potential type you choose, for
some of the potentials (the pivot-free ones) you do not have to provide a u
vector, since it is calculated on the fly as the center of positions or
as the center of mass (depending on whether you choose mass-weighting or not
with the rot_massw0 parameter).

If you have more than one protein that you want to constrain the rotation for,
set rot_ngroups to a value larger than 1 and provide values for each group 
in rot_vec0, rot_vec1, and so on.
> 
> I suppose that in order to just keep the direction of the v axis during the 
> dynamics, my choise have to be rote_rate=0, is it correct?
Yes, and you have to choose a spring constant (k, or rot_k0) that determines how
close your protein stays at the given angle, i.e. how large you allow
the fluctuations about the angle to be.

Good luck!
  Carsten
> 
> 
> Thanks again,
> 
> Anna
> 
> 
> 
> 
> 
> 
> 
> 
>> ----Messaggio originale----
>> Da: ckutzne at gwdg.de
>> Data: 25/07/2013 11.12
>> A: "battistia at libero.it"<battistia at libero.it>
>> Cc: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>> Ogg: Re: [gmx-users] Rotation Constraints - PMF - external potential
>> 
>> On Jul 24, 2013, at 5:53 PM, battistia at libero.it wrote:
>> 
>>> Dear Carsten
>>> 
>>> could you give me more information about your suggestions?
>>> I tried but probably I did not understand well what you meant.
>> Hi Anna,
>> 
>> I suggested to use the enforced rotation module of Gromacs 4.6
>> to restrain the orientation of your molecule(s). If you want to
>> use the orientation restraints module instead, I am afraid I
>> can not help you much with that, maybe someone else on this list? 
>> 
>>> In order to avoid the rotation of the structure A and of the structure B,  
> I 
>>> have defined into the index file a group A_B that contains A+B and  I have 
>>> setted in the mdp file the following parameters:
>>> 
>>> ; Orientation restraints: No or Yes
>>> orire                    = yes
>>> ; Orientation restraints force constant and tau for time averaging
>>> orire-fc                 = 500
>>> orire-tau                = 100
>>> orire-fitgrp             = A_B
>>> ; Output frequency for trace(SD) and S to energy file
>>> nstorireout              = 100
>>> 
>>> As I have synthetically described in the first post , the structures A and 
> B 
>>> (characterized by a cylindrical shape) are defined by a number of 32  unit-
>>> structures that I call s.
>>> 
>>> Into the itp is defined the topology for the s structure, and so in order 
> to 
>>> put an orientation restraints between atoms that are not included into the 
> same 
>>> itp file,
>>> I cannot put into the topology a section like that described into the 
> manual 
>>> 4.6.2 pag. 92 namely,  [ orientation_restraints ],  could I ?
>>> 
>>> Could you tell me How I can fix the orientation of the systems A and B?
>> Using the enforced rotation module you would choose an index group and an 
> axis 
>> for each group that you want to fix the orientation, set the rotation angle 
> to 
>> zero and choose an appropriate force constant. Appropriate potential 
> functions
>> would be the pivot-free ones if I understand your setting correctly.
>>> 
>>> I don't understand the manual's explanation about the   orire-fitgrp:
>>> (fit group for orientation restraining. This group of atoms is used to 
>>> determine the rotation
>>> R of the system with respect to the reference orientation. The reference 
>>> orientation is the
>>> starting conformation of the first subsystem. For a protein, backbone is a 
>>> reasonable choice)
>>> 
>>> How one have to give the group? using an index file or defining the group 
> in 
>>> the topology?
>> This is the "orire-fitgrp = A_B" mdp file setting that you made.
>> 
>> Best,
>> Carsten
>>> 
>>> 
>>>> ----Messaggio originale----
>>>> Da: ckutzne at gwdg.de
>>>> Data: 23/07/2013 13.09
>>>> A: "battistia at libero.it"<battistia at libero.it>, "Discussion list for 
> GROMACS 
>>> users"<gmx-users at gromacs.org>
>>>> Ogg: Re: [gmx-users] Rotation Constraints - PMF
>>>> 
>>>> Hi Anna,
>>>> 
>>>> please have a look at the Enforced Rotation Section in the Gromacs 4.6 
>>> manual.
>>>> You can restrain the angle of rotation about an axis by setting the 
> rotation 
>>> rate
>>>> to zero. There is also a 4.5 add-on available with rotational restraints 
> in
>>>> the Gromacs git repository (branch "rotation"). For more info you may want 
> to
>>>> look at this page:
>>>> 
>>>> http://www.mpibpc.mpg.de/grubmueller/rotation
>>>> 
>>>> Best,
>>>> Carsten
>>>> 
>>>> 
>>>> On Jul 23, 2013, at 12:18 PM, battistia at libero.it wrote:
>>>> 
>>>>> Dear user and expert,
>>>>> I'd like ask you a suggestion about a problem that I will try present 
> you 
>>> schematically.
>>>>> I have got a structure "s" and I have generated the topolgy file itp for 
> it.
>>> A number of separate "s" in turn generate a complex structure A, that is 
>>> characterized by a cylindrical shape.
>>>>> Now, I constructed a system with two cylindrical structures, A and B (in 
>>> total made by 64 "s" structures), and I'd like make an Umbrella Sampling 
>>> calculation in order to study the PMF varying the distance between A and B.
>>>>> 
>>>>> My problem is that I'd like fix the orientation of the axis of each 
>>> structure A and B long the z axis, during the dynamics.
>>>>> So I need to put a force into the system or a constrain, such that when 
> the 
>>> axis of A or B rotates respect to z axis, the force puts back the axis of 
> the 
>>> structure in the z direction.
>>>>> 
>>>>> It this possible?  If it is so, could you tell me how to do that?
>>>>> Than you very much,
>>>>> Anna
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
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>>>> 
>>>> 
>>>> --
>>>> Dr. Carsten Kutzner
>>>> Max Planck Institute for Biophysical Chemistry
>>>> Theoretical and Computational Biophysics
>>>> Am Fassberg 11, 37077 Goettingen, Germany
>>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>>>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>> 
>> 
> 
> 


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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